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An Information Theoretic Approach to Constructing Robust Boolean Gene Regulatory Networks

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2012年第1期9卷 52-65页

作者： Vasic, Bane Ravanmehr, Vida Krishnan, Anantha Raman Univ Arizona Dept Elect & Comp Engn Inst Collaborat Biores BIO5 Tucson AZ 85721 USA Univ Arizona Dept Math Tucson AZ 85721 USA Western Digital Corp Irvine CA 92612 USA

We introduce a class of finite systems models of gene regulatory networks exhibiting behavior of the cell cycle. The network is an extension of a Boolean network model. The system spontaneously cycles through a finite set of internal states, tracking the increase of an external factor such as cell mass, and also exhibits checkpoints in which errors in gene expression levels due to cellular noise are automatically corrected. We present a 7-gene network based on Projective Geometry codes, which can correct, at every given time, one gene expression error. The topology of a network is highly symmetric and requires using only simple Boolean functions that can be synthesized using genes of various organisms. The attractor structure of the Boolean network contains a single cycle attractor. It is the smallest nontrivial network with such high robustness. The methodology allows construction of artificial gene regulatory networks with the number of phases larger than in natural cell cycle.

关键词： Gene regulatory networks Boolean networks cell cycle error correction error correction coding

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Comparing Analytical, Micromagnetic and Statistical Channel Models at 4 Tcbpsi Patterned Media Recording

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IEEE TRANSACTIONS ON MAGNETICS 2012年第5期48卷 1826-1832页

作者： Chua, M. Elidrissi, M. R. Eason, K. Zhang, S. H. Qin, Z. L. Chai, K. S. Tan, K. P. Cai, K. Chan, K. S. Goh, W. L. Dong, Y. Victora, R. H. ASTAR Data Storage Inst Singapore 117608 Singapore Nanyang Technol Univ Sch Elect & Elect Engn Singapore 637457 Singapore Univ Minnesota Ctr Micromagnet & Informat Technol Dept Elect & Comp Engn Minneapolis MN USA

Bit patterned media recording (BPMR) is a candidate technology proposed to extend the areal density growth capability of magnetic recording systems. In conventional granular magnetic recording (CGMR), bits of information are recorded onto a number of randomly distributed magnetic grains. The difficulty for the granular media approach is that due to the randomness of the grains, a certain minimum number of grains are required in order to maintain the media signal to noise ratio (SNR). This requires smaller grains as the bits are shrunk and we end up with either unstable, or unwriteable grains as per the well-known media-trilemma. In BPMR, instead of random positions, the "grains" are ordered into a well-defined lattice of magnetic islands. Because of this ordering, the media SNR is no longer determined by the number of grains per bit as in CGMR, but is defined by the geometrical and magnetic distributions of the fabrication process of the media. Analytical models exist for BPMR, that flip grains in the media based on the switching field distribution (SFD) and the knowledge of the applied head field. On the other side, a statistical model for CGMR has been proposed that measures probabilities of grains flipping based on micromagnetic simulations, named the grain flipping probability (GFP) model. In this work, we adapt the GFP model for BPMR and perform a comparison between densities predicted via the analytical and GFP models, by processing the signals from these models with the appropriate detectors and LDPC (low density parity check) decoders.

关键词： Codes error correction error correction coding error detection coding signal processing

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An area efficient LDPC decoder using a reduced complexity min-sum algorithm

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INTEGRATION-THE VLSI JOURNAL 2012年第2期45卷 141-148页

作者： Chandrasetty, Vikram Arkalgud Aziz, Syed Mahfuzul Univ S Australia Sch Elect & Informat Engn Mawson Lakes SA 5095 Australia

Hardware implementation of Low-Density Parity-Check (LDPC) decoders using conventional algorithms such as Sum-Product or Min-Sum requires large amount of hardware resources. A rather simplistic way to reduce hardware resources is to reduce the intrinsic message quantization. However this adversely affects the bit error rate (BER) performance significantly. In this paper, a resource efficient LDPC decoder based on a reduced complexity Min-Sum algorithm is presented. It reduces the inter-connect complexity by restricting the extrinsic message length to 2 bits and also simplifies the check node operation. Simulation at the algorithmic level shows that the proposed decoder achieves BER performance better than that of a 3-bit Min-Sum decoder, and therefore addresses the problem of massive BER performance degradation of a 2-bit Min-Sum decoder. The reduction in algorithmic complexity and further hardware optimization of the variable node leads to significant savings in hardware resources compared to 3-bit Min-Sum. An LDPC decoder with a code length of 1152 bits has been implemented on a Xilinx FPGA using the proposed algorithmic and hardware enhancements. With a 0.1 dB BER performance gain to that of 3-bit Min-Sum decoder, the proposed decoder saves about 18% of FPGA slices and provides a higher throughput. (C) 2011 Elsevier B.V. All rights reserved.

关键词： Digital communication error correction coding Iterative decoding Field programmable gate array Logic design

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Message length adaptive LDPC codes

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DIGITAL SIGNAL PROCESSING 2012年第6期22卷 1107-1112页

作者： Tiwari, Honey Durga Cho, Yong Beom Konkuk Univ Dept Elect Engn Seoul 143701 South Korea

LDPC codes achieve better performance and lower decoding complexity than turbo codes, with a major drawback of high encoding complexity. The encoder generator matrix is derived from the inverse of portion of parity check matrix. If the message length is changed, the structure of parity check matrix is modified and hence, the generator matrix must be re-computed. This increases the encoding complexity as the computation of matrix inverse is time and resource consuming operation. In this paper, we consider the encoding problem for LDPC codes as the complexity of encoding is essentially quadratic wills respect to the block length. Using an efficient encoding method proposed by Richardson and Urbanke, we propose a systematic procedure to construct parity check matrix and generator matrix such that with change in message length, the re-computation for constructing generator matrix is avoided. The presented design uses fixed sub-matrices to construct a semi-random parity check matrix. The resultant design will reduce the pre-computation time of converting parity check matrix to generator matrix. The reported encoder reduces encoding time without the loss of coding gain and Bit error Rate (BER) performance. (C) 2012 Elsevier Inc. All rights reserved.

关键词： error correction coding Low-density parity check codes Permutation matrix

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Low-Complexity Soft Decoding of Huffman Codes and Iterative Joint Source Channel Decoding

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IEEE TRANSACTIONS ON COMMUNICATIONS 2012年第6期60卷 1669-1679页

作者： Zribi, Amin Pyndiah, Ramesh Zaibi, Sonia Guilloud, Frederic Bouallegue, Ammar Natl Engn Sch Tunis Commun Syst SysCom Lab Tunis 1002 Tunisia Univ Europeenne Bretagne Signal & Commun Dept UMR CNRS 6285 Inst TelecomTelecom BretagneLab STICCCS 83818 F-29238 Brest 3 France

Most source coding standards (voice, audio, image and video) use Variable-Length Codes (VLCs) for compression. However, the VLC decoder is very sensitive to transmission errors in the compressed bit-stream. Previous contributions, using a trellis description of the VLC codewords to perform soft decoding, have been proposed. Significant improvements are achieved by this approach when compared with prefix decoding. Nevertheless, for realistic VLCs, the complexity of the trellis technique becomes intractable. In this paper, we propose a soft-input VLC decoding method using an a priori knowledge of the lengths of the source-symbol sequence and the compressed bit-stream with Maximum A Posteriori (MAP) sequence estimation. Performance in the case of transmission over an Additive White Gaussian Noise (AWGN) channel is evaluated. Simulation results show that the proposed decoding algorithm leads to significant performance gain in comparison with the prefix VLC decoding besides exhibiting very low complexity. A new VLC decoding method generating additional information regarding the reliability of the bits of the compressed bit-stream is also proposed. We consider the serial concatenation of a VLC with two types of channel code and perform iterative decoding. Results show that, when concatenated with a recursive systematic convolutional code (RSCC), iterative decoding provides remarkable error correction performance. In fact, a gain of about 2.3 dB is achieved, in the case of transmission over an AWGN channel, with respect to tandem decoding. Second, we consider a concatenation with a low-density parity-check (LDPC) code and it is shown that iterative joint source/channel decoding outperforms tandem decoding and an additional coding gain of 0.25 dB is achieved.

关键词： Communication system performance source coding variable-length codes error correction coding iterative methods

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100G and Beyond Transmission Technologies for Evolving Optical Networks and Relevant Physical-Layer Issues

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PROCEEDINGS OF THE IEEE 2012年第5期100卷 1065-1078页

作者： Ip, Ezra Ji, Philip Mateo, Eduardo Huang, Yue-Kai Xu, Lei Qian, Dayou Bai, Neng Wang, Ting NEC Labs Amer Princeton NJ 08540 USA Univ Cent Florida CREOL Orlando FL 32816 USA

As 100-Gb/s/lambda digital coherent systems enter commercial deployment, an effort is underway to uncover the technologies that will enable the next-generation optical fiber communication systems. We envisage that future optical transport will be software-defined, enabling flexible allocation of bandwidth resources, with dynamically adjustable per-channel data rates based on instantaneous traffic demand and quality-of-service requirements, leading to unprecedented network agility. Software-defined transponders will have the programmability to adopt various modulation formats, coding rates, and the signal bandwidth based on the transmission distance and type of fiber. Digital signal processing will become increasingly ubiquitous and sophisticated, capable of compensating all types of channel impairments, enabling advanced forward error correction coding, and performing functions previously handled poorly by optical analog hardware such as spectrum shaping and demultiplexing of optical channels.

关键词： Coherent detection digital signal processing error correction coding fiber optic communications modulation formats multimode fibers multicore fibers nonlinear compensation optical time division multiplexing optical signal processing orthogonal frequency division multiplexing single mode fibers space division multiplexing

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Non-Binary Coded Modulation and Iterative Detection for High Spectral Efficiency in MIMO

Non-Binary Coded Modulation and Iterative Detection for High...

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46th Asilomar Conference on Signals, Systems and Computers

作者： Chang, Nicholas B. Romero, David L. MIT Lincoln Lab Lexington MA 02420 USA

ISBN: (纸本)9781467350518

Non-binary low density parity check codes (LDPC) have been shown to outperform their binary counterparts and attain the best-known performance among error-correction codes. At the same time, it has also been established that wireless communication using multiple-input multiple-output (MIMO) schemes dramatically increases system capacity and reliability when information symbols are appropriately coded and modulated across transmit antennas. Recent works have studied techniques for applying non-binary LDPC codes to MIMO systems and demonstrated near-capacity performance. However, the constellation sizes in the proposed approaches are limited by the Galois field (GF) size of the non-binary LDPC code, thus limiting the maximum spectral efficiency of the proposed joint modulation-coding approaches. In practice, the GF size may be limited by computational complexity reasons but high spectral efficiencies are desired. Thus, we study iterative coded modulation based techniques for applying non-binary LDPC codes to higher order modulations. These methods have been well-studied for binary codes but not for non-binary codes. It is demonstrated that performance of the technique is dependent on the mapping of GF symbols to constellations, but applying the appropriate mapping attains near-capacity performance. To reduce the error floor region for smaller field sizes, while maintaining steep waterfall curves, we combine a nonbinary-based accumulator with a parallel concatenated coding scheme.

关键词： error correction coding nonbinary low-density parity-check space-time coding multiple-input multiple-output (MIMO) iterative detection factor graph belief propagation

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A Joint Layered Scheme for Reliable and Secure Mobile JPEG-2000 Streaming

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ACM TRANSACTIONS ON MULTIMEDIA COMPUTING COMMUNICATIONS AND APPLICATIONS 2012年第3期8卷 30-30页

作者： Zhu, Xinglei Chen, Chang Wen SUNY Buffalo Dept Comp Sci & Engn Buffalo NY 14260 USA

This article presents a novel joint layered approach to simultaneously achieve both reliable and secure mobile JPEG-2000 image streaming. With a priori knowledge of JPEG-2000 source coding and channel coding, the proposed joint system integrates authentication into the media error protection components to ensure that every source-decodable media unit is authenticated. By such a dedicated design, the proposed scheme protects both compressed JPEG-2000 codestream and the authentication data from wireless channel impairments. It is fundamentally different from many existing systems that consider the problem of media authentication separately from the other operations in the media transmission system. By utilizing the contextual relationship, such as coding dependency and content importance between media slices for authentication hash appending, the proposed scheme generates an extremely low authentication overhead. Under this joint layered coding framework, an optimal rate allocation algorithm for source coding, channel coding, and media authentication is developed to guarantee end-to-end media quality. Experiment results on JPEG-2000 images validate the proposed scheme and demonstrate that the performance of the proposed scheme is approaching its upper bound, in which case no authentication is applied to the media stream.

关键词： Algorithms Performance Security Multimedia authentication authentication schemes mobile media communication communication system security error correction coding streaming authentication

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Soft-decision forward error correction for 100 Gb/s digital coherent systems

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OPTICAL FIBER TECHNOLOGY 2011年第5期17卷 452-455页

作者： Onohara, Kiyoshi Sugihara, Takashi Miyata, Yoshikuni Sugihara, Kenya Kubo, Kazuo Yoshida, Hideo Koguchi, Kazuumi Mizuochi, Takashi Mitsubishi Electr Corp Kamakura Kanagawa 2478501 Japan

Soft-decision forward error correction (SD-FEC) and its practical implementation for 100 Gb/s digital coherent systems are discussed. In applying SD-FEC to a digital coherent transponder, the configuration of the frame structure of the FEC becomes a key issue. We present a triple-concatenated FEC, with a pair of concatenated hard-decision FEC (HD-FEC) further concatenated with an SD-based low-density parity-check (LDPC) code for 20.5% redundancy. In order to evaluate error correcting performance of SD-based LDPC code. We implement the entire 100 Gb/s throughput of LDPC code on field programmable gate arrays (FPGAs) based hardware emulator. The proposed triple-concatenated FEC can achieve a Q-limit of 6.4 dB and a net coding gain (NCG) of 10.8 dB at a post-FEC bit error ratio (BER) of 10 (15) is expected. In addition, we raise an important question for the definition of NCG in digital coherent systems with and without differential quadrature phase-shift keying (QPSK) coding, which is generally used to avoid phase slip caused by the practical limitations in processing the phase recovery algorithms. (C) 2011 Elsevier Inc. All rights reserved.

关键词： error correction coding Field programmable gate arrays Forward error correction Optical communication Parallel processing

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Impact of Approximation error on the Decisions of LDPC Decoding

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JOURNAL OF SIGNAL PROCESSING SYSTEMS FOR SIGNAL IMAGE AND VIDEO TECHNOLOGY 2011年第1期64卷 41-59页

作者： Kanistras, Nikos Paliouras, Vassilis Univ Patras Dept Elect & Comp Engn Patras 26500 Greece

In this paper the impact of the approximation error on the decisions taken by LDPC decoders is studied. In particular, we analyze the mechanism, by means of which approximation error alters the decisions of a finite-word-length implementation of the decoding algorithm, with respect to the decisions taken by the infinite precision case, approximated here by double-precision floating-point. We focus on four popular algorithms for LDPC decoding, namely Log Sum-Product, Min-Sum, normalized Min-Sum and offset Min-Sum. A corresponding theoretical model is developed which derives an expression for the probability of altering the decision due to approximation. The model is applied to the above algorithms for the case of the first iteration as well as for higher numbers of iterations. Finally, experimental results prove the validity of the proposed model.

关键词： Low-density parity-check (LDPC) codes Finite-word-length effects error correction coding

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